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from ase.calculators.calculator import Parameters
"""
2017.04 - Pedro Brandimarte: changes for python 2-3 compatible
"""
class PAOBasisBlock(Parameters):
"""
Representing a block in PAO.Basis for one species.
"""
def __init__(self, block):
"""
Parameters:
-block : String. A block defining the basis set of a single
species using the format of a PAO.Basis block.
The initial label should be left out since it is
determined programatically.
Example1: 2 nodes 1.0
n=2 0 2 E 50.0 2.5
3.50 3.50
0.95 1.00
1 1 P 2
3.50
Example2: 1
0 2 S 0.2
5.00 0.00
See siesta manual for details.
"""
assert isinstance(block, str)
Parameters.__init__(self, block=block)
def script(self, label):
"""
Write the fdf script for the block.
Parameters:
-label : The label to insert in front of the block.
"""
return label + ' ' + self['block']
class Species(Parameters):
"""
Parameters for specifying the behaviour for a single species in the
calculation. If the tag argument is set to an integer then atoms with
the specified element and tag will be a separate species.
Pseudopotential and basis set can be specified. Additionally the species
can be set be a ghost species, meaning that they will not be considered
atoms, but the corresponding basis set will be used.
"""
def __init__(self,
symbol,
basis_set='DZP',
pseudopotential=None,
tag=None,
ghost=False,
excess_charge=None):
kwargs = locals()
kwargs.pop('self')
Parameters.__init__(self, **kwargs)
def format_fdf(key, value):
"""
Write an fdf key-word value pair.
Parameters:
- key : The fdf-key
- value : The fdf value.
"""
if isinstance(value, (list, tuple)) and len(value) == 0:
return ''
key = format_key(key)
new_value = format_value(value)
if isinstance(value, list):
string = '%block ' + key + '\n' +\
new_value + '\n' + \
'%endblock ' + key + '\n'
else:
string = '%s\t%s\n' % (key, new_value)
return string
def format_value(value):
"""
Format python values to fdf-format.
Parameters:
- value : The value to format.
"""
if isinstance(value, tuple):
sub_values = [format_value(v) for v in value]
value = '\t'.join(sub_values)
elif isinstance(value, list):
sub_values = [format_value(v) for v in value]
value = '\n'.join(sub_values)
else:
value = str(value)
return value
def format_key(key):
""" Fix the fdf-key replacing '_' with '.' and '__' with '_' """
key = key.replace('__', '#')
key = key.replace('_', '.')
key = key.replace('#', '_')
return key
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